Classic Shell: Forum

First off please excuse my lack of knowledge or correct terminology.

My OS is Win 8 Pro (staying away from 8.1 as long as humanly possible), i5 2400 CPU, 120GB SSD, & a GTX 670. Its almost exclusively used for gaming.

I've been using Classic Shell on my & many of the peoples PC's we look after without incident for months, but...

I downloaded the latest version of Classic Shell & installed it giving permission to close explorer (which I've done on 2 previous update occasions without any problem).
When explorer restarted...

• The task bar links were inoperable,
• The file permissions were reset to most items.
• The profile information for Firefox was unable to be located.
• The library links to folders ie: documents, music etc were empty & failed to open.
  
  I restored my system to a few hours before but the changes are registry based which is where I'm a little bit of a novice.
  
  After restart the task bar links were white & empty.
  
  I decided to go back & re-download the latest version in case it got corrupted.
  
  I've attempted to reset the exe & other essential files using a DVD image I have for such occurrences (usually only used in relation to Trojan & Malware/Spyware attacks) but the DVD drive is inoperable.
  
  These are the classic symptoms of a Trojan attack but I'm sure its an easy fix if I'm pointed in the right direction. I'd rather not re-install so, HELP
  
  Now I've had some problems recently with various versions of Avast blocking items it shouldn't & generally behaving badly.
  
  If you need any other info I'll be checking back every so often.
  
  Thanks in advance.
  
  To Add:

To regain my permissions, reclaim ownership of my files/programs & to have the DVD recognise DVDs again, I ran FixExec by Lawrence Abrams initially, & now I'm running tweaking.com all-in-one repair, will post the results on restart.

15/01/2014
OK ran a few tools including the ones listed above.
I had to create a direct link from Program\ files firefox folder to the desktop as not all the desktop exe's still not all working.
I had to take ownership of the shortcuts again to enable them. IE: utorrent, google chrome & a few others.

Seems its a bit of a mystery.

I would definately suggest naking a registry back up before updating anything from now on, including classic shell.